2I0A

Crystal Structure of KB-19 complexed with wild type HIV-1 protease

Summary for 2I0A

• Entry DOI: 10.2210/pdb2i0a/pdb
• Related: 1F7A 2I0D
• Descriptor: Protease, PHOSPHATE ION, (5S)-3-(4-ACETYLPHENYL)-N-[(1S,2R)-1-BENZYL-2-HYDROXY-3-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}PROPYL]-2-OXO-1,3-OXAZOLIDINE-5-CARBOXAMIDE, ... (5 entities in total)
• Functional Keywords: drug design, hiv-1 protease, protease inhibitors, hydrolase
• Biological source: Human immunodeficiency virus 1
• Total number of polymer chains: 2
• Total formula weight: 22741.30

Authors

Nalam, M.N.L.,Schiffer, C.A.,Ali, A.,Reddy, K.K.,Cao, H.,Anjum, S.G.,Rana, T.M. (deposition date: 2006-08-10, release date: 2006-12-19, Last modification date: 2023-08-30)

Primary citation

Ali, A.,Reddy, G.S.,Cao, H.,Anjum, S.G.,Nalam, M.N.,Schiffer, C.A.,Rana, T.M.
Discovery of HIV-1 Protease Inhibitors with Picomolar Affinities Incorporating N-Aryl-oxazolidinone-5-carboxamides as Novel P2 Ligands.
J.Med.Chem., 49:7342-7356, 2006

PubMed Abstract: Here, we describe the design, synthesis, and biological evaluation of novel HIV-1 protease inhibitors incorporating N-phenyloxazolidinone-5-carboxamides into the (hydroxyethylamino)sulfonamide scaffold as P2 ligands. Series of inhibitors with variations at the P2 phenyloxazolidinone and the P2' phenylsulfonamide moieties were synthesized. Compounds with the (S)-enantiomer of substituted phenyloxazolidinones at P2 show highly potent inhibitory activities against HIV-1 protease. The inhibitors possessing 3-acetyl, 4-acetyl, and 3-trifluoromethyl groups at the phenyl ring of the oxazolidinone fragment are the most potent in each series, with K(i) values in the low picomolar (pM) range. The electron-donating groups 4-methoxy and 1,3-dioxolane are preferred at P2' phenyl ring, as compounds with other substitutions show lower binding affinities. Attempts to replace the isobutyl group at P1' with small cyclic moieties caused significant loss of affinities in the resulting compounds. Crystal structure analysis of the two most potent inhibitors in complex with the HIV-1 protease provided valuable information on the interactions between the inhibitor and the protease enzyme. In both inhibitor - enzyme complexes, the carbonyl group of the oxazolidinone ring makes hydrogenbond interactions with relatively conserved Asp29 residue of the protease. Potent inhibitors from each series incorporating various phenyloxazolidinone based P2 ligands were selected and their activities against a panel of multidrug-resistant (MDR) protease variants were determined. Interestingly, the most potent protease inhibitor starts out with extremely tight affinity for the wild-type enzyme (K(i) = 0.8 pM), and even against the MDR variants it retains picomolar to low nanomolar K(i), which is highly comparable with the best FDA-approved protease inhibitors.

PubMed: 17149864
DOI: 10.1021/jm060666p

Experimental method

X-RAY DIFFRACTION (1.8 Å)